The incumbent's only challenger was Hama Amadou, who was obliged to campaign from behind bars after being detained on November 14 on what many observers have said were likely trumped-up baby-trafficking charges. Issoufou said they were concocted to derail his election bid.
Amadou was also flown to France days before the second round for medical treatment. His medical condition is unclear, but his health reportedly deteriorated in prison.
The electoral commission said on Tuesday - presenting official preliminary results - that Issoufou claimed 92.5 percent of the vote, against around 7 percent for Amadou.
Turnout had become a key issue given the opposition boycott. The opposition COPA 2016 coalition said national turnout was a mere 11 percent nationwide, but the official initial estimate put participation at 56 percent.
The 64-year-old Issoufou won 48.4 percent in the first round on February 21, with Amadou gaining 17.7 percent.
One of the world's poorest countries, Niger faces a growing jihadist threat and has recently come under concerted attack by militants from al-Qaeda and Boko Haram.
Issoufou, who took office in 2011, campaigned on promises to bring prosperity to the impoverished uranium-rich country. He also vowed to put a stop to further attacks from jihadists in the country's vast and remote north and from Nigeria's Boko Haram Islamists in the south.
Issoufou was elected as the first president of the Seventh Republic following the adoption of a new constitution and presidential elections in 2010.
jh/msh (Reuters, AFP)